NEWS

PhysioStream 0.9.4

A vignette carries one task end to end on synthetic or bundled data, offline, and is built and run by R CMD check.
Runnable @examples added or corrected across 75 help pages. Each runs offline in seconds, writes nothing outside tempdir(), and is executed by R CMD check; anything needing a device, a download or an optional backend is fenced with the reason stated.
The README's quick start runs as written: it attaches the package, builds its own inputs, and uses only hard dependencies.

bandpassRmsOp() crashed on a matrix with no column names -- the most natural thing to hand a pipeline -- because naming the output computed paste0(NULL, "_rms"), length one, against a multi-column matrix. The same NULL also served as the not-yet-initialised flag, so an unnamed stream reset its filter state on every chunk, silently discarding the carried zi and RMS window. Channel names are synthesised once as Ch1..Chn and initialisation is tracked explicitly.

XDF writing and stream synchronisation accept the canonical MultiPhysioExperiment. They previously tested for MultiRatePhysioExperiment only, which would have rejected a container built by the current constructor.

Made two tests portable to the macOS/Windows r-universe binary builders (which the 0.9.1 pyxdf-skip fix exposed once those tests stopped being masked): (1) the bundled-JS syntax check now asserts node --check exits 0 rather than requiring silent output, since macOS/Windows node emits deprecation/experimental warnings orthogonal to syntax validity (and skips when node is absent); (2) the DSP reference-fixture covariance self- consistency check uses a numeric tolerance (1e-8) instead of tolerance = 0, because stats::cov() is BLAS/LAPACK-backed and drifts ~1 ULP across platforms.

Fixed XDF/LSL capability probes triggering reticulate's automatic ephemeral Python provisioning. reticulate (>= 1.41) downloads uv, CPython and NumPy on first initialization when no interpreter is configured; on an offline build machine (e.g. r-universe binaries) that network work fails/hangs, so the pyxdf/pylsl skip guards surfaced as test ERRORs instead of clean SKIPs. The probes now gate on an already-configured, on-disk interpreter (py_discover_config() / py_available(initialize = FALSE), neither of which provisions) and never start a download. Tests skip cleanly when no Python backend is present.

Add governed loopback, MQTT v5, serial TTL, and callback TTL stimulation-command outlets with explicit side-effect-free construction and transport lifecycle.
Add arm, heartbeat/dead-man, channel maximum, duration, duplicate-command, and per-channel refractory software gates with sealed bounded audit state.
Record conservative unknown delivery after transport invocation, never retry stimulation commands automatically, and distinguish transport acknowledgement from physical stimulation.

Add bounded synchronous stream pipelines with transactional per-chunk callback state and explicit error/drop-oldest/drop-newest backpressure.
Add process-local monotonic ingest-to-emit latency records and p50/p95/p99 benchmark summaries.
Add a compiled causal SOS-bandpass plus rolling-RMS operation for the documented 32-channel latency reference chain.

Add governed LMS, normalized LMS, and recursive-least-squares adaptive filters with inspectable coefficient and delay state.
Add constant-memory incremental PCA and adaptive-whitening online ICA.
Add exponentially weighted online Welch spectra and sliding STFT/band-power emission with exact chunk-boundary continuity.
Add portable hashed processor-state snapshots, transactional updates, and independent per-channel causal-filter integration.

Add serializable robust clock-offset models with reset-segment drift correction and bounded extrapolation.
Add explicit timestamp de-jittering that preserves sample values, counts, order, and reset boundaries.
Add governed multi-stream synchronization and residual/jitter/event diagnostics for MultiRatePhysioExperiment containers.

Add capability-gated XDF import through pinned pyxdf while preserving native file, stream-header, footer, clock, and timestamp evidence.
Add an atomic native XDF 1.0 writer for governed numeric and string streams.
Map every XDF stream to a PhysioExperiment inside a common-clock MultiRatePhysioExperiment, including lossless marker payloads and events.

Add capability-gated pylsl discovery with governed LSL descriptor, channel, rate, dtype, source, and clock-domain mapping.
Add reference-like LSLInlet and LSLOutlet endpoints with strict lifecycle, payload, timestamp, and local overwrite accounting.
Add bounded irregular string-marker capture and deterministic conversion to PhysioEvents.
Add offline metadata fixtures, independent validation, and optional real localhost loopback coverage for all governed LSL dtypes.

Add validated StreamInfo, virtual source/sink contracts, and deterministic loopback streams.
Add a bounded native SPSC ring buffer with explicit overwrite accounting.
Add governed PhysioExperiment snapshots that preserve acquired timestamps and sequence identity.